Version 4.1

3D Imaging Systems
Your Guide to the Widest Selection of
Optical Sectioning, Electron Microscopy and X-ray Microscopy Techniques.

// INNOVATION    MADE BY ZEISSThe moment
your data change
scientific minds.
This is the moment we work for.

Identify Your Competitive Advantages

Simpler. More intelligent.
More integrated. Focused on results.
3D imaging is a key part of your most demanding experiments. Your microscopes shouldreflect that, whether you work in a multi-user facility or a one person laboratory.
With ZEISS you will always have the best techniques to hand. From the largest family of
3D imaging systems. And with ZEISS, you will also have partners who can look at yourquestions with you. Who will take your needs and advise you in a straightforward way.
Who are with you for the initial start-up of your microscope system and will continue
to keep it up to date. The name ZEISS is your promise of products that are easy to use,
­intelligent, and fully integrated. Our passion is backed by over a century and a half of solid
achievements, and it shows – recognize this in how deeply and comprehensively we­support you before, during, and after you decide on ZEISS. Find out more about our­support services on page 65.

Bridging the Micro and Nano Worlds
Maximize Your Options with Correlative Microscopy –More Flexibility. Greater Speed. Increased Throughput.

At ZEISS, correlative microscopy is not so much about the technology you are usingas the questions you are asking. Essential questions that define your research in the life
sciences. Questions that drive you to probe ever deeper into a specimen until you reveal
the answers within. In these pages you will find a product portfolio that ranges from zoom
microscopes to confocal Laser Scanning Microscopes (LSM) and superresolution systems
to Scanning Electron Microscopes (SEM), Crossbeam (FIB-SEM) and X-ray microscopy (XRM)
solutions. Simply transfer your specimens from one instrument to another and relocate
the regions of interest (ROIs) in next to no time. Or image large areas and h­ undreds of­sections across length scales and combine them into one single correlative volume data
set. Use correlative solutions from ZEISS to connect microscopy techniques, resolution
ranges and 3D imaging modalities to answer your scientific questions.

7Build Your System to Your Exact Requirements.
In these pages, you will see the world’s widest selection oflight, electron and X-ray microscopes for 3D imaging andthe different technologies behind it. Think about what matters
to you. Then use this knowledge to select your ideal system.

8

Light Microscopy
Image your samples with 3D light microscopy techniques:• Widefield Deconvolution• Multiphoton Microscopy• Structured Illumination• Airyscanning• Light Sheet Fluorescence Microscopy• Superresolution PALM

• Spinning Disk

• Superresolution SIM• Laser Scanning Microscopy
Page 10

Correlative Microscopy
Combine structural and functional information of your biological samples:• Shuttle & Find
• ZEN Correlative Array Tomography• Atlas 5 Array Tomography

Page 38

Electron Microscopy
Reconstruct your biological samples in 3D with nanometer resolution:• Focused Ion Beam Scanning Electron Microscopy (FIB-SEM)• Field Emission – SEM (FE-SEM) with integrated ultramicrotome• Atlas 5 Array Tomography

Page 44

X-ray Microscopy
Visualize your biological samples in their native state in 3D:• X-ray Microscopy

Page 549

Light Microscopy

Image Your Samples with
3D Light Microscopy Techniques

10

11

Light Microscopy

Light microscopes from ZEISS use­advanced excitation and detection­options to support even your mostdemanding experiments.

Widefield Deconvolution Uses
All Emitted Light
Widefield deconvolution microscopes are one of the most sensitive
solutions for live cell imaging and acquire both the in-focus andout-of-focus light contributions from a specimen.
Making use of knowledge of the point spread function (PSF),
3D deconvolution calculates light in image stacks back to its placeof origin. This increases contrast and even the dimmest of structures
are made visible.
3D deconvolution is both a very light efficient and cost-effective
approach to generate 3D data.

12

Structured Illumination with

A Light Sheet Excites Only What You Image

Grid Pattern Projection
In structured illumination microscopy a grid is projected into theLight sheet microscopy lets you acquire images of your whole

focal plane of a widefield fluorescence microscope. The image of­sample volume at sub-cellular resolution in a fraction of the time it

the grid is precisely moved in the lateral direction, and several

takes with other techniques. Fluorescence excitation and detection­images are acquired at the focal plane, each with the grid in ais split into two separate light paths, with the axis of illumination­d ifferent position. Since fluorescence emission from areas inperpendicular to the detection axis. That means only a single thinfocus varies more significantly per position than emission fromsection of the sample is illuminated, generating an inherent optical

out-of-focus areas, it is possible to automatically create an opticalsection by exciting only fluorescence from the in-focus plane.

section that is free from out-of-focus blur. While it takes more

No pinhole or image processing is required. Light from the in-focus

time to acquire a single focal plane than with the 3D widefieldplane is rapidly acquired by a sensitive camera. High speed acquisi-­deconvolution approach, this technique does not require totion combined with minimal laser excitation allow to image

collect image stacks. It also offers greater levels of out-of-focus­specimens in 3D over days with virtually no phototoxicity or photo-

discrimination.

bleaching.

13

Light Microscopy

The Spinning Disk
Rotates with Hundreds of Pinholes
A spinning disk system projects the excitation light simultaneously
through hundreds of pinholes into your specimen and collects
the returning emission through the same confocal apertures.
Emission light is blocked by the disk and you get an optical­section. Spinning disk systems are confocal systems working in­parallel and record multiple spots of the specimen at high speed
and increased resolution. They are ideal for observing cellular­processes.

14Confocal Laser Scanning

Multiphoton Excitation Concentrates the Light

Delivers Superb Optical Sectioning
With a laser scanning microscope, you create optical sections point

Multiphoton Microscopes, or Non Linear Optics (NLO), rapidly scanby point as the system passes a point of light over the field of view

the single beam of a pulsed, ultrafast and tunable laser across theat high speed. A pinhole allows only emission light from the focal

sample. The IR excitation wavelengths range from about 700 nm

plane to pass through and contribute to the image. While single-

to over 1,100 nm. It thus becomes highly probable only in the

point scanning is slower than parallel scanning, it gives you great­focal spot that two or more photons excite a fluorophore in a

flexibility to choose experimental setups, image sizes and acquisi-­similar way to a single photon with typically half the wavelength.

tion strategies. It also offers the highest out-of-focus discrimina-­Outside the focus the laser intensity drops exponentially and doestion of all routine optical sectioning techniques.

not excite fluorophores. Thus, the confocal aperture is no longer
needed to reject out-of-focus light. The emitted light can be­collected much more efficiently and the infrared wavelengths thatare used can penetrate much deeper into tissue. T­ ogether, these
aspects make multiphoton systems the state of the art for i­maging
deep tissue layers with subcellular resolution.

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Light MicroscopyEnter a New World of Confocal Performance with
AiryscanningWith Airyscan you get the unrivaled combination of fast super­
resolution and sensitive image acquisition in a confocal system.
Use multicolor samples with any label and get image quality likeyou’ve never seen before. Decide on this novel detector design
and get a 4 – 8× improvement in signal-to-noise ratio (SNR)
while s­ imultaneously achieving a 1.7× increase in resolution.
You will even profit from this unique combination of greater
SNR and r­ esolution at increased acquisition speeds of 27 fps at
480 × 480 pixels.

16

50 nmXenopus laevis, A6 cells (epithelial kidney cells). Stained for gp210, a nuclear pore

Widefield image (left) and SIM image (right) of a Brp (Bruchpilot) antibody staining

complex protein with 8 fold radial symmetry with secondary antibody system

in neuromuscular junctions of Drosophila larvae.

­conjugated to Alexa 647. Courtesy of A. Löschberger and M. Sauer, University of

Courtesy of H. Aberle and C. Klämbt, University of Münster, Germany

Würzburg, Germany

PALM: Enjoy the Highest Resolution in Light Microscopy

SR-SIM: Get Superresolution for All Standard Dyes

Photoactivated Localization Microscopy (PALM) is your method

Superresolution Structured Illumination Microscopy (SR-SIM)of choice to explore ultrastructural details of cellular objects.

is your ideal entry point to investigate your structure at double

Moreover, by localizing single molecules with high precision, their

the resolution in all dimensions compared to classical widefield

distribution as well as their abundance get accessible for analysis.

­imaging. Unlike other superresolution techniques only minimal

TIRF or HILO illumination offer you the best possible signal inlight doses are required so your sample will not be harmed

two or even three dimensions. You can achieve ten times higher

by ­imaging. What’s more, SR-SIM works with all establishedresolution when using an optimally prepared sample.

­fluorophores or dyes.

17Light Microscopy

ZEISS Cell Observer: Long-term Experiments with High Frame Rates
Your Technology: Widefield Deconvolution

Configured to Your Requirements
Life sciences research demands high-performance imaging

Microscopes

systems. You want to remain flexible and be able to operate

Inverted: Axio Observer 7

each of the functions of your system easily.
Excitation Options
Cell Observer from ZEISS lets you acquire simple time-lapse

HXP 120 V, HBO, XBO or Colibri 7,

images and carry out multidimensional setups for your complex

fast switchable Xenon lamps (DG-4)

heterogeneous experiments. With just one platform, you can­acquire long-term experiments reliably and achieve high frame

Accessories

rates, thanks to streaming and precise synchronization with yourPiezo focus, filter wheels, shutters, scanning stages, hardware

external devices.

­focus stabilizer, flexible incubation setups, high-resolution andhighly sensitive CCD cameras, EMCCD and sCMOS cameras for

As your requirements grow, you can upgrade your Cell Observer –highest s­ ensitivity, dual camera option for fastest speed andfor example, with the confocal spinning disk unit or with Apotome.2­maximum ­efficiency

for optical sectioning.
Software
ZEN system with additional modules: Tiles & Positions, Panorama,
Experiment Designer, Deconvolution, 3D VisArt, Image Analyis,
Macro Environment, Advanced Processing & Analysis, Physiology

18Four Dictyostelium cells stably transformed with a GFP construct (imaged) shortly

Fixed brain sections from somatosensory cortex of GAD67-GFP transgenic

after spore germination in vegetative state. You can recognize the typical formation

mouse stained with antibodies to somatostatin and parvalbumin.

of pseudopodia for this stage. Courtesy of R. Gräf, University of Potsdam, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• From long-term time-lapse imaging to fast 3D acquisition, a broad• Image live cells with the whole spectrum of fluorescent

range of applications let you do it all with one single device.
• Acquire even the faintest signals in live cells at high frame rates.
LEDs work as excitation light sources with the lowest possible
phototoxicity. The TTL-controlled synchronization of the dual
camera option makes sure both images are acquired at exactly
the same time. You will work more efficiently in your processes
and save time, too.
• Cell Observer combines fast acquisition, 3D deconvolution,
3D rendering, and important measurement tools.

proteins with highest sensitivity.
• Follow intracellular trafficking events at high speed ina quantitative representation.
• Take images with the dual camera option and perform
simultaneous, quantitative ion or FRET imaging.
• Capture morphological changes at high spatial resolution
using deconvolution.
• Investigate cell cycles quantitatively using long-term
microscopy with minimal phototoxicity.

The system supports cameras from other manufacturers as wellas Axiocams.

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Light Microscopy

ZEISS Celldiscoverer 7: Your Automated Platform for Live Cell Imaging
Your Technology: Widefield Deconvolution

Configured to Your Requirements
Often in life sciences research, the data you are after will only be

Microscopes

revealed through multiple runs of experiments or complex assays.

Boxed inverted: Celldiscoverer 7

Automation and parallelization can be the only way to get there.
Now, with Celldiscoverer 7, you can combine the easy-to-use

Detection Options­automation of a boxed microscope with the image quality andAxiocam 503 mono, Axiocam 506 mono, Axiocam 512 mono,

flexibility of a classic inverted research microscope.

Axiocam 702 mono and a range of sCMOS and EMCCD cameras

Celldiscoverer 7 calibrates itself, then detects and focuses on yourAccessories

samples while adaptive optics adjust themselves. Leaving you free

Autoimmersion, various incubation options (incl. cooling, perfusion

to get on with other projects.

and dispensing), robotic plate loader

Whether working with 2D or 3D cell cultures, tissue sections

Softwareor small model organisms, you will acquire better data in shorter

ZEN celldiscoverer includes modules for multi-dimensional image

times with this reliable automated research platform.

acqusition, Tiles & Positions, Experiment Designer, advanced image
processing and a­ nalysis tools
Recommended additional modules:
GPU-based deconvolution (GPU-DCV),
3Dxl Viewer – powered by arivis®,

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Open application development (OAD)

Rat cortical primary neuron culture. Antibody-staining of bIII-tubulin (Cy2, green),

Live cricket embryos (Gryllus bimaculatus). Nuclear-localized GFP. Movements andNestin (Cy3, red) and DCX (Cy5, purple). Nuclei Dapi-stained (blue). Maximum intensity­divisions of single cells throughout the embryo during development. Sample courtesy

projection of a Z-stack (left image: widefield, right image: deconvolved).

of S. Donoughe, Biological Labs,Harvard University, Cambridge, USA

Sample courtesy of H. Braun, LSM Bioanalytik GmbH, M­ agdeburg, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Controlled environment allows uncompromised live cell imaging.

• Investigate cellular processes quantitatively using long-term• Acquire even the faintest signals in live cells at high frame rates.
Use LEDs for imaging with low phototoxicity. Experience
the best performance in keeping your samples healthy overextended periods of time.
• Celldiscoverer 7 combines advanced automation, high performance dedicated optics, fast acquisition, 3D deconvolution,
3D rendering, measurement tools and interfaces for external
software and hardware components.

microscopy with minimal phototoxicity.
• Follow intracellular trafficking events at high speed ina quantitative representation.
• Image live cells with the whole spectrum of fluorescentproteins with highest sensitivity.
• Analyze cell cultures in 2D and 3D with elevated throughput
in a variety of different sample carriers.
• Capture morphological changes at high spatial resolution
using deconvolution.

21

Light Microscopy

ZEISS Apotome.2 Delivers Crisp Optical Sections
Your Technology: Structured Illumination

Configured to Your Requirements
Simply insert Apotome.2 into the field stop position – it’s that easy

Microscopes

to create optical sections with your widefield fluorescence system.

Upright: Axio Imager.Z2, Axio Imager.M2, Axio Imager.A2,
Axio Zoom.V16

Apotome.2 uses structured illumination to create optical sections.

Inverted: Axio Observer 7, Axio Observer 5, Axio Observer 3

As the module projects a grid pattern into the focal plane, thesystem calculates your optical section from three or more images

Excitation Options

with different grid positions. Apotome.2 also removes out-of-focus

HXP 120 V or Colibri 7

blur, even in thicker samples.

Free choice of fluorescence filter sets

Apotome.2 is your system of choice if you want a convenient

Accessories

way to acquire multichannel images from tissue sections. It also

Three grids matching the chosen objectives;

creates perfect 3D images of whole organisms. You get brilliant

3D Deconvolution module for ZEN imaging software

images with optimal contrast in the best possible resolution.

included for resolution improvement

Yet your widefield system remains as easy to operate as always.
Software
ZEN system with additional modules: Tiles & Positions,
Experiment Designer, Colocalisation, 3Dxl Viewer – powered by arivis®,
Image Analysis, TimeLapse, Z Stack

22

Mitotoc HeLa cells. Blue: DNA, stained with Hoechst 33342; Green: Tubulin, stained

Neuromuscular junctions of Drosophila. Green: synapses, stained with Alexa 488;

with Alexa 488; Red: ACA, stained with Alexa 568.

red: muscles, stained with Alexa 568; white: motor neurons, stained with Alexa 647;
blue: nucleus, stained with Hoechst 33258. Courtesy of K. VijayRaghavan,
National Centre for Biological Sciences, TIFR Centre, Bangalore, India

Simpler. More intelligent. More integrated.

Created for Your Applications• Just insert Apotome.2 into the field stop position to produce• Display multicolor neuronal branching in brain sections.

optical sections.
• These optical sections are calculated and displayed online.
• With the fully-automatic grid selection you get optical sections
with optimal thickness for all objective magnifications.
• It works with most standard white-light sources for fluorophores
ranging from UV to near infrared – or use the Colibri 7 LED lightsource and achieve unsurpassed contrast.
• Use the Deconvolution module (included) to make a significant
improvement in resolution of raw data.

• Research the formation of tissue in embryos with low
phototoxicity.
• Scan large objects automatically with the ZEN module
Tiles & Positions.
• Capture subcellular structures in three dimensions withan easy-to-use setup and short acquisition times.
• Analyze the localization of multiple fluorescence markers
in pathological sections without out-of-focus blur.
• Increase the image resolution by up to 30 %using the Deconvolution module.

23

Light Microscopy

ZEISS LSM 800 with Airyscan: Your Compact Confocal for High-End Imaging
Your Technology: Single-point Laser Scanning

Configured to Your Requirements
Confocal imaging demands the very best imaging quality.

Microscopes

With LSM 800 you are choosing a flexible and compact confocal

Upright: Axio Imager.Z2, Axio Imager.M2, Axio Examiner.Z1*

laser scanning microscope, complete with highly sensitive GaAsPInverted: Axio Observer 7

detector technology and fast linear scanning. Add Airyscan, therevolutionary detection concept from ZEISS, and you will gain

Excitation Options

1.7× higher resolution in all three dimensions – resulting in a

Use either two (488 / 561 nm) or

5× smaller confocal volume. And you will be pushing sensitivity

four laser lines (405, 488, 561 and 640 nm),beyond the limits of all conventional confocals.

use HXP 120 or Colibri 7 for widefield excitation

LSM 800 is your entry into the world of high-end confocal

Scanning Modules and Accessories­imaging. Simply decide which options your system needs today,

LSM 800 with two or three confocal detectors and built-in

then upgrade in the future as your needs grow.

spectral flexibility;
Options: Airyscan for LSM 800, transmitted light detection,­Definite Focus.2, Autocorr objectives;
Software
ZEN with additional modules: Tiles & Positions, Experiment Designer,(*available on request)

3Dxl Viewer – powered by arivis®, Deconvolution, Macro Environment, Experiment Feedback, FRET / FRAP Analysis, Shuttle & Find

24

3D dataset of an optical lobe of the Drosophila brain; labelled with three antibodies:

Comparison between confocal (left) and Airyscan (right) image. HeLa cells, red: mito-

Alexa 488, 568 and 633. Sample: courtesy of D. Reiff, Insitute of Biology, Albert-­

chondria membrane, green: microtubuli, magenta: actin fibers. Sample: ­courtesy of

Ludwigs-University Freiburg, Germany

A. Seitz, BioImaging and Optics Core Facility, EPFL, Lausanne, Switzerland

Simpler. More intelligent. More integrated.

Created for Your Applications• The compact design delivers the superb image quality of• Acquire up to 3 channels simultaneously for

the LSM 8 family with a small footprint and an excellent
price / performance ratio.
• Airyscan delivers 1.7× higher resolution in x, y and z ­without
sacrificing sensitivity or speed.
• Up to three GaAsP detectors give you the greatest flexibility forlive cell imaging.
• Well defined interfaces to third party software and the inte­
grated OAD platform for scripting allow seamless integration

multi-fluorescence colocalization analyses.
• Perform long-term 3D live cell imaging with highly sensitive
GaAsP detectors or Airyscan at minimal laser exposure.
• Analyze molecule interaction and dynamics with FRET and
FRAP including photoactivation and photoconversion.
• Correlate functional data from LSM 800 withultrastructural information from your ZEISS SEM with theZEN module Shuttle & Find.

into existing infrastructure and a high degree of personalization.

25

Light Microscopy

ZEISS LSM 880 with Airyscan:Your New Standard for Fast and Gentle Confocal Imaging
Your Technology: Single-point Laser Scanning

Configured to Your Requirements
To get ahead in your research you may want to image the smallest

Microscopes

structures, catch the faintest signal or track the fastest processes –Upright: Axio Imager.Z2, Axio Imager.M2; Axio Examiner.Z1

or do all of that at once. When it comes to getting accurate data

Inverted: Axio Observer 7

from live cells or other weakly-labeled samples, there is no suchthing as too much sensitivity, resolution or speed. Each photon of

Excitation Options

emission light is precious.

UV laser: 355 nm, 405 nm

With Airyscan you have the unrivaled combination of superresolu-

VIS laser:	440 nm, 458 nm, 488 nm, 514 nm, 543 nm, 561 nm,

tion and sensitive confocal image acquisition at hand. Airyscan in

594 nm, 633 nm

Fast mode combines unrivaled image quality and superresolution

NIR laser for multiphoton imaging: Ti:Sa: 690 nm – 1,080 nmwith high acquisition speed to answer your scientific questions.

OPO, InSight Deep See, Discovery or second TiSa Laser *Use multicolor samples with any label and get a 4 – 8× improve-

Scanning Modules and Accessories

ment in signal-to-noise ratio (SNR) as compared to imaging with

3 or 34 descanned spectral channels (GaAsP and / or PMT);

conventional confocal GaAsP detectors. And 1.7× higher resolu-

Airyscan detector with optional Fast module; 2 additional GaAsPtion for your single photon or multi-photon experiments.

­channels (BiG.2); Definite Focus.2; up to 12 non-descanned GaAsPor PMT detectors; Transmitted light detector (T-PMT); Autocorr objectives(*available on request)

Software
ZEN with additional modules: Tiles & Positions, Experiment Designer,

26

FRAP, FRET, RICS, FCS, Deconvolution, 3Dxl Viewer – powered by arivis®

HeLa cells, Actin stained with Phalloidin-Alexa 546, AP3 with Alexa 488, DAPI.

Apis mellifera. Hypopharyngeal gland secretory cell, cryosectioned and labelled

Left: state-of-the-art GaAsP detection; right: Airyscan detection.

with AlexaFluor 488-phalloidin (green) and 2°AB-Cy3 membrane marker (magenta).

Courtesy of S. Traikov, BIOTEC, TU Dresden, Germany

The ring-like structures (green) have a diameter of about 2.5 μm.
Courtesy of O. Baumann, University of Potsdam, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Use Airyscan to get superresolution imaging with high sensitivity• Acquire multi-fluorescence images and analyze colocalization

at 140 nm laterally and 400 nm axially. This transcends theat the same time as you are performing spectral imaging­deconvolution approach by preserving precious emission lightof fluorescent proteins.

normally rejected at a closed pinhole.
• Speed up your imaging by a factor of four - with Airyscan’s• Perform 3D live cell imaging with enhanced resolution and SNRover long periods of time.

unique Fast mode. This will propel you into the traditional• Analyze molecule interaction and dynamics with FRET, FRAP,­domain of resonant scanning confocals without sacrificing

and FLIP, including photo­activation and photoconversion.

­sensitivity or resolution.
• Image deep within tissue using gentle multiphoton excitationand get the benefits of increased sensitivity and resolution with

• Use the innovative RICS software to analyze individual
molecules. Use FLIM with pulsed lasers in the 405 / 440 nm
range, tuneable from 488 to 640 nm, and anisotropy imaging.

GaAsP – NDDs, Airyscan or Airyscan Fast mode.
• Working with identical pixel times and continuous scanner­monitoring, you can perform quantitative imaging at all speeds
and scan modes at any scan field rotation.
• Collect all your fluorescent signals in one go. Parallel acquisitionlets you investigate multiple labels in minimum time, equippedwith the highest number of detectors of any confocal.

27

Light Microscopy

ZEISS Lightsheet Z.1 for Multiview Imaging of Large SpecimensYour Technology: Light Sheet Fluorescence Microscopy

Configured to Your Requirements
Lightsheet Z.1 uses a pure form of optical sectioning microscopy to

Microscopes

capture stunning images from very large volumes with gentle illu-

Dedicated boxed horizontal systemmination of the focal plane only. Every aspect of Lightsheet Z.1 has
been tailored to create the ultimate platform for both imaging of

Excitation Options

large cleared tissues and long-term observation of live samples.

Up to 6 laser lines: 405, 445, 488, 515, 561 and 638 nm;

The unique sample handling allows the collection of Z-stacks fromchoose from lasers with different power levels

the perfect angle of viewing – or from a number of different angles, in multiple positions and with different zoom factors. Stream-

Detection Modules and Accessories

ing of data to storage and processing computers allows to handle

Single or dual camera acquisition with sCMOS cameras

large data sets and makes processing easy. You can image whole

for best speed and sensitivity, scalable integrated incubation

organisms faster and longer than ever before.

solution, sample holders and sample chambers
Software
ZEN system with additional modules: MultiView Acquisition
and Reconstruction, Deconvolution, 3Dxl Viewer – powered by arivis®,
arivis Vision4D

28

Brain of an adult Drosophila, Maximum intensity projection rendered from 4 views.

Maximum intensity projection of a 3D rendering of a 2 day old living Zebrafish

Magenta: proboscis muscles, stained with Rhodamine phalloidin; red: neuroglian,heart. The 2 channel fluorescence image dataset shows the blood vessels andstained with Alexa 647; green: GFP-neurons, stained with Alexa 488.

the endocardium labeled in red. The myocardium is labeled in green.

Courtesy of A.A. Bohra and K. V. Raghavan, NCBS, Bangalore, India

Courtesy of M. Mickoleit, Huisken lab, MPI CBG, Dresden, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Perform parallel or sequential imaging• Image the development of whole organisms in 3D over days.

with single or dual camera solutions.
• Image your fluorescent specimens with• Perform long-term time-lapse imaging with virtually no
phototoxicity or photobleaching.

the sealed system in open and well-lit laboratories.

• Visualize dynamic subcellular organelles with fast acquisitions.

• It’s easy to handle and process large amounts of data

• Image 3D cell cultures without the constraint of a coverslip.

with the integrated offline workstation.

• Image optically cleared specimens.

• Control all environmental conditions with
ZEN imaging software and adjust to the needsof even your most demanding samples.

29

Light Microscopy

ZEISS Cell Observer SD Captures the Pulse of LifeYour Technology: Spinning Disk

Configured to Your Requirements
With Cell Observer SD, you have it all. The image quality ofMicroscopes

Axio Observer and Axio Examiner. Spinning disk technology from

Upright: Axio Examiner.Z1

Yokogawa CSU-X1. And the dual camera technology of ZEN

Inverted: Axio Observer 7­imaging software. This symbiosis of optics, hardware and software
in one ­system makes your confocal live cell imaging uniquely­accurate: you can control your Cell Observer SD precisely in the
millisecond range. By streaming image data, you will acquire yourimages in breathtakingly short times. You can also document two
fluorescence channels of your sensitive samples simultaneously andget even more valuable data.

Excitation Options
Up to 6 laser lines: 405, 445, 488, 515, 568, 640 nm;
each laser module can be equipped with either a single or fast­switching triple fiber output
Accessories
Fast emission filter wheel, dual camera acquisition with CCD, E­ MCCD
and sCMOS cameras, various EMCCD cameras for the best detection
sensitivity, scalable and laser-safe incubation solutions, DirectFRAP­laser manipulation slider for dynamic photoactivation and photobleaching, fast switching laser module, hardware focus stabilizer(for inverted microscope only)
Software
ZEN system with additional modules: Tiles & Positions, Panorama,­Experiment Designer, Deconvolution, 3Dxl Viewer – powered by arivis®,
Image Analysis, Macro Environment, Advanced Processing & Analysis,

30

Dynamics

Zebrafish embryo development. Maximum intensity projection from a single time point

HeLa cells. Plan-APOCHROMAT 63× / 1.4. Microtubuli end-binding protein:of a 10-hour time-lapse acquisition. Plan-APOCHROMAT 25× / 0.8 LD LCI. Membrane

EGFP (green), H2B: mCherry (red)stained with Tg (-8.0cldnb:lynGFP) (green), nuclei are labeled with mCherry (red).
Courtesy of J. Otte, M. Takamiya, and U. Strähle, Karlsruhe Institute of Technology, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Use software-controlled incubation to manage environmental• Image subcellular trafficking in 3D over time withconditions for displaying live cells.
• Streaming technology lets you observe dynamic cell processes
at high frame rates.
• All components are seamlessly integrated and controlledwith millisecond accuracy.
• Parallel or sequential imaging, and one or two camera­solutions available.

maximum acquisition speed.
• Visualize cytoskeletal dynamics with the highest sensitivity.
• Carry out photobleaching experiments with the optional
DirectFRAP unit.
• Perform functional imaging of cellular signaltransduction at high temporal resolution.
• Accomplish long-term confocal live cell imaging
with lowest phototoxicity.

31

Light Microscopy

ZEISS Elyra P.1: Investigate Ultrastructural Details at theSingle Molecule Level
Your Technology: Photoactivated Localization Microscopy (PALM)

Configured to Your Requirements
With Elyra P.1 you can analyze structures within sections andMicroscopes

cultured cells down to the molecular level. Image single molecule

Inverted: Axio Observer 7

fluorescence with highest sensitivity and at well beyond the­d iffraction limit.

Excitation Options
Laser lines 405 nm (50 mW), 488 nm (100 or 200 mW),

Use TIRF illumination for best signal-to-noise in 2D PALM imaging.

561 nm (100 or 200 mW), and 642 nm (150 mW);

For 3D PALM experiments, it’s easy to switch to HILO illumination.

HXP 120 for widefield excitationOr, use PRLIM (Phase Ramp Localization Imaging Microscopy)
method for a high capture range.

Accessories
Laser-safe incubation solutions, special TIRF objective withextra-high NA (1.57), combination with Elyra S.1, combination with
LSM 880 with Airyscan, many customized filter configurations, fullymechanically controlled phase ramp slider
Software
ZEN system and additional modules: 3Dxl Viewer – powered by arivis®,
Deconvolution, Photoactivated Localization Microscopy

32

50 nmXenopus laevis, A6 cells (epithelial kidney cells). Stained for gp210, a nuclear poreU2OS (human Osteosarcoma) cell. Stained for centriolar protein CEP152 withcomplex protein with 8 fold radial symmetry) with secondary antibody systema ­secondary antibody system conjugated to Alexa 647. Courtesy of T. Klein,­conjugated to Alexa 647. Courtesy of A. Löschberger and M. Sauer, University of

University of Würzburg, Germany

Würzburg, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Capture quantitative data with inherent single molecule analysis• Analyze the ultrastructure of subcellular compartments.

for each image.
• Match the power density to the needs of your experiment.
• Choose your illumination scheme for best sensitivity(TIRF, HILO, EPI).
• Detect structural details as fine as 20 – 40 nm in lateral and• Measure molecule numbers and their proximity within astructure.
• Track molecules to derive their dynamics.
• Map molecule distribution and clustering with a structuralcontext.

60 – 80 nm in axial direction.
• Combine PALM with SR-SIM and confocal systems.

33

Light Microscopy

ZEISS Elyra S.1: Double the Resolution in 3 Dimensions
Your Technology: Superresolution Structured Illumination Microscopy (SR-SIM)

Configured to Your Requirements
Elyra S.1 achieves up to twice the resolution compared to

Microscopes

conventional systems for optical sectioning. Using SR-SIM you will

Inverted: Axio Observer 7

gain new insights into your regular samples. A rotating lightpattern is the core of this superresolution technique. From a small

Excitation Options

stack of widefield data, your system calculates images with aLaser lines 405 nm (50 mW), 488 nm (100 or 200 mW),

resolution improvement in both xy as well as z directions.

561 nm (100 or 200 mW), and 642 nm (150 mW);
HXP 120 for widefield excitation
Accessories
Laser-safe incubation solutions, combination with Elyra P.1,
combination with LSM 880, customized filter configurations
Software
ZEN system and additional modules: 3Dxl Viewer – powered by arivis®,
Tiles & Positions, Deconvolution, Structured Illumination34

Widefield image (left) and SIM image (right) of neuronal growth cones stained for

Widefield image (left) and SIM image (right) of a Brp (Bruchpilot) antibody staining

tubulin (red) and F-actin (green).

in neuromuscular junctions of Drosophila larvae.

Courtesy of M. Fritz and M. Bastmeyer, University of Karlsruhe, Germany

Courtesy of H. Aberle and C. Klämbt, University of Münster, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Choose freely from among all common fluorescent proteins• Image multiple fluorophores and analyze colocalizations.

and dyes to achieve superresolution.
• Create Z-stacks with improved axial resolution – up to twice
as much as is possible with conventional microscopes for
optical sectioning.
• Display colors with up to four channels in superresolution.
• Combine Elyra S.1 with Elyra P.1 and confocal systems to
enjoy total flexibility.

• Analyze cells and small whole-mount or sectioned samples
with 3D superresolution.
• Analyze chromatin structures with DAPI and up to three
additional 3D super-resolved channels for immunostaining
or fluorescence in-situ hybridization (FISH).
• Display fluorescent protein expression inside yeast withoutstanding resolution.

35

Light Microscopy

ZEISS LSM 880 with Airyscan and Elyra PS.1:
Your Platform for Far-reaching Answers
Your Technology: Confocal and Superresolution Microscopy

Configured to Your Requirements
With Elyra PS.1 you benefit from the synergy of two powerful

Microscopes

superresolution techniques. Determine the distribution of ­proteins

Inverted: Axio Observer 7

within a structural context or get quantitative data by counting
single molecules.

Excitation Options

Add Airyscan to combine three powerful superresolution techniques

Laser lines 405 nm (50 mW), 488 nm (100 or 200 mW),on one platform. You will have the advantages of true optical

561 nm (100 or 200 mW), and 642 nm (150 mW);

­sectioning and now you can even image samples in superresolution

laser module shared between PALM and SR-SIM;

which are too thick or dense to be analyzed with PALM or SIM.

HXP 120 for widefield excitation
Accessories
Laser-safe incubation solutions, customized filter configurations36

8C nucleus of Arabidopsis leaf cell stained with Alexa 647 for active non-phos­

8C interphase nucleus of Arabidopsis stained for centromeric repeats by FISH using

phorylated RNA polymerase II (Pol II). The SIM image (in green) reveals a reticulate

Alexa 488. Imaging by SIM (white) gives the distribution of the repeats, whereas

structure of Pol II within the Chromatin. The PALM image (in red) demonstrates

counting by PALM (yellow) reveals their abundance. Veit Schubert, IPK Gatersleben,­clustering of the molecule. Courtesy of V. Schubert, IPK Gatersleben, Germany

Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Choose the superresolution technique that best answers• Analyze the distribition of molecules within a structural context.

your question.
• Combine the power of two of the best superresolution
techniques for optimum information gain.
• Combine Elyra PS.1 with LSM 880 and Airyscan to join theworlds of widefield and confocal superresolution techniques.

• Reveal the precise location of single molecules on cellular
structures.
• Analyze a substructure within an object and observe finest
details.
• Map the contribution of different classes of proteins to the
make-up of an organelle.

37Correlative Microscopy

Combine Structural and Functional
Information from Your Biological Samples

38

39

Correlative Microscopy

ZEISS Shuttle & Find: Combine Functional and Structural Information
Your Technology: Correlative Microscopy

Configured to Your Requirements
All you need is a sample such as fluorescent-labeled cells,

Microscopes

ultrathin sections or whole blocks of tissue.

Light microscopes: Stereo, zoom and widefield microscopeswith motorized stage, LSM 8 family, Elyra

Complement images of fluorescent-labeled cellular components

Electron microscopes: SEM family

acquired in a light microscope with ultrastructural informationfrom your electron microscope.

Accessories
SEM Adapter

Shuttle & Find, the correlative approach from ZEISS, lets you

Sample holder for coverslips or TEM grids

decide which imaging solutions are best suited to your needs.
Using ­specifically-designed correlative holders or coverslips with

Softwarededicated software, it’s easy to transfer the sample and correlated

Light microscopes: ZEN Shuttle & Find

your data, making the relocation of selected regions of interests

Electron Microscopes: ZEN Shuttle & Find, SmartSEM(ROIs) fast and easy.

40

Makrophages feeding on fluorescent beads ranging in size from 5 to 1 μm, cell culture

Correlation of SIM-, dSTORM and SEM images after automated recovery withon ITO glass coverslip. Overlay image: LM DIC and fluorescencewith SEM, SE2 image.

Shuttle & Find. High pressure freezing, resin embedded, ultrathin sections,

Courtesy of K. Czymmek and J. Caplan, Delaware Biotechnology Institute, University

ultramicrotome, on ITO cover slips. Courtesy of K. Czymmek, J. Caplan, Delawareof Delaware, USA

Biotechnology Insitute, University of Delaware, USA

Simpler. More intelligent. More integrated.

Created for Your Applications• Increase productivity with Shuttle & Find. In just a few easy steps• Investigate the ultrastructure of your specimens.

you can relocate ROIs within the two microscope systems.

• Extract information from even smallest yeast cells.

The software module stores ROIs marked in the light microscope• Image ultrathin sections.

together with their coordinates and then finds them in seconds• Analyze subcellular structures.

in the electron microscope.
• Combine data from your Elyra superresolution system with datafrom your SEM.
• The modular approach of Shuttle & Find lets you capitalize on
the full flexibility of both your light microscope and SEM.

41

Correlative Microscopy

ZEN Correlative Array Tomography:
3D Correlative Light and Electron Microscopy For Serial Sections
Your Technology: Correlative Microscopy

Configured to Your Requirements
Array Tomography uses serial sections to reconstruct your sample

Microscopes

volume. Use an ultramicrotome to cut your resin-embedded tissue

Light Microscopes: Axio Imager.Z2, Axio Observer 7,

samples into consecutive sections and image them. Precise auto-

Electron Microscopes: GeminiSEM 300 / 500, Sigma 300 / 500,

matic alignment of the secion images allows 3D reconstruction of­Merlin, Merlin Compact, Auriga, Supra, Ultra

your sample. The section thickness determines the z-resolution.
The unique software module ZEN Correlative Array Tomography

Accessories

enables you to connect your light and electron microscopes.

Specimen holder CorrMic Life Sciences for cover glasses 22 × 22 mm,

After automated image acquisition in the light microscope, you

SEM Adapter for Specimen holder CorrMic Life Sciences,

can transfer the sample to your electron microscope where you

ZEISS Cover Glasses with Fiducials

find the same software tools. Then you can automatically image
hundreds of sections across length scales and combine them into

Softwareone single correlative volume dataset.

Light microscopes: ZEN (blue edition), ZEN module Correlative­Array Tomography, ZEN 3Dxl Viewer – powered by arivis®
Electron Microscopes: SmartSEM, ZEN SEM (Basis software),ZEN SEM Module Correlative Array Tomography42

Correlation of the LM z-stack with the SEM z-stack. The distribution of the hunting-

3D reconstruction of serial sections from root nodules with the distribution of plas-

tin plaques and the location of the nucleus is clearly visible in 3D.

modesmata. Cell wall: blue (Calcofluor white); Plasmodesmata: red (anti-ß-Glucan).
Courtesy of D. Sherrier, J. Caplan, and S. Modla, University of Delaware, USA

Simpler. More intelligent. More integrated.

Created for Your Applications• Perform large-scale 3D correlative microscopy.

• Investigate the ultrastructure of your specimens in 3D.

• Simply outline one of the sections in your ribbon and ZEN• Image tens to hundreds of ultrathin sections.

Correlative Array Tomography will detect and mark all other• Analyze subcellular structures in their 3D context.

sections automatically.
• Outline the region of interest (ROI) in any of your sections.
The software suggests the optimal tiling setup and automaticallytransfers the ROI to all other sections.

43Electron Microscopy

Reconstruct Your Biological Samples
in 3D with Nanometer Resolution

44

45

Electron Microscopy

Electron microscopy is your methodof choice for 3D imaging of tissues,
cells and molecules at nanometer
resolution.
Depending on the application you haveseveral options for acquiring 3D data.
You can cut your sample into ultrathin
sections and image them individually.
Or use Array Tomography for fully automated imaging. Perform block-face imaging with a focused ion beam (FIB-SEM).
Or use the integrated ultramicrotome
to remove the surface of the sample
slice by slice directly in your scanning

FIB-SEM

electron microscope (SEM).

Whether you work with resin-embedded or vitrified cryo samples,
nanotomography simplifies your life. Use the ion beam to cut into
your sample and uncover information lying in the depth.
Just define a cutting region and let the ion beam do the rest.
The ion beam removes slices as thin as 5 nm or even less from thesurface, giving you full control of your section thickness when­acquiring 3D image stacks.
Take advantage of Crossbeam’s simultaneous milling and imaging
capability. You can correlate results observed in your light microscope by relocating your region of interest and acquiring 3D­Crossbeam data at the same location – no additional ultramicrotomy
required. In addition, it’s easy to access subvolumes identified forfurther TEM or STEM investigation by preparing thin lamellas.

46

Ultramicrotome Integrated in the SEM Chamber

Investigate Near-to-Native Biological Samples

For larger samples, take advantage of the speed and ease-of-use

Native morphology can only be observed when you freeze yourof the ultramicrotome inside the chamber of your SEM.

sample instead of using chemical fixatives. The main objective in

Use it to remove a slice from the surface of your resin-embedded

cryo electron microscopy is to prepare a biological sample in its

tissue sample. Afterwards an image of the block-face will behydrated state. Vitrification at liquid nitrogen temperature keeps­acquired automatically using the FE-SEM – at a resolution of just a

the ultrastructure fully intact. Thus your sample remains completely

few nm. This process is then repeated automatically for thousands

hydrated. No additional fixation or embedding is needed.

of sections. The microtome operates without interruption for hours

Plunge freezing and high pressure freezing are well-establishedor even days, acquiring volume data of your sample in a fully auto-

methods to fix your biological sample for further investigations inmated process.

the electron microscope. ZEISS supports all necessary equipment
for transferring the sample at cryo conditions into the electron
microscope.

47

Electron Microscopy

ZEISS Crossbeam: Block-Face Imaging
for Tissue Samples Using a Focused Ion BeamYour Technology: Focused Ion Beam Scanning Electron Microscopy

Configured to Your Requirements
Crossbeam technology provides a complete 3D imaging system forElectron Microscopes

your biological samples. It combines the imaging performance of

Crossbeam 550, Crossbeam 540, Crossbeam 340

the renowned GEMINI column with the milling capability of asuperior FIB. Designed for high throughput and high resolution,
Crossbeam brings you all the benefits of a modular platform with
an open software architecture.

Technology
GEMINI based Field-Emission Scanning Electron Microscopy (FE-SEM)
Detection Possibilities
Various detection modes for secondary electron imaging, secondary
ion imaging, analytical imaging, energy selective backscatter imaging
Milling Technology
Capella column for multi-purpose applications and best FIB resolution
Options
Local Charge Compensation for imaging of non-conductive
samples, Inlens EsB detector for finest z resolution without
topographic artifacts, Airlock for fast and efficient sample transfer,flood gun, variable pressure mode
Software
SmartSEM, Atlas 548

3D nanotomogram generated from ~300 consecutive, 10 nm thick FIB-SEM sections

Cryo FIB-SEM of a vitrified mouse optic nerve. The image represents a slice out ofof resin embedded Trypanosoma brucei. Courtesy of S. Vaughan, Brookes University,

a 3D volume of 127 consecutive FIB sections covering 7.5 µm × 5.7 µm × 3.8 µm

Research Group “Cell biology of trypanosomes”, Oxford, UK(pixel size 7.5 nm × 7.5 nm with 30 nm slice thickness). Courtesy of W. Möbius, MPI
Göttingen, Germany

Simpler. More intelligent. More integrated.

Created for Your Applications• Its modular platform concept lets you configure the Crossbeam• Get isotropic structural information from your biological sample

precisely to your applications.
• Image your samples with high resolution and magnetic-field
free with the unique GEMINI technology.
• Innovative FIB-technology gives you access to up to five ordersof magnitude of beam current, enabling fast and precise
material removal and a milling process with best z-resolution.
• Capitalize on live FE-SEM monitoring for perfect control of yourin 3D with voxel sizes smaller than 5 nm in each direction.
• Speed up your 3D data acquisition by selectively imaging
regions.
• Identify the native structure of your biological sample byimaging the specimen in a frozen state under cryo conditions.
• Investigate interfaces in samples with different material
hardness for biomedical engineering.

entire FIB-processing.
• Use local charge compensation for imaging of non-conductive
biological samples.
• Speed up your 3D data acquisition with Atlas 5. Take advantage
of flexible definition of regions of interest within a frame of
50 k × 40 k pixel per slice at variable resolutions including
3D drift tracking.

49Electron Microscopy

ZEISS Sigma 3View and ZEISS Merlin 3View:
Block-Face Imaging for Tissue Samples Using an UltramicrotomeYour Technology: Field Emission Scanning Electron Microscopy (FE-SEM)

Configured to Your Requirements
Combine your Merlin or Sigma VP with 3View® technology

Electron Microscopesfrom Gatan Inc. to acquire high resolution 3D data from resin-­

Sigma 300 VP, GeminiSEM 300, Merlin *embedded cell and tissue samples. You’ll get results in the shortest
possible time and the most convenient way. 3View® is an ultra­

Sectioning Technique Hardware

microtome inside the SEM chamber.

Ultramicrotome 3View® XP:
Cut thickness down to 15 nm, automated image acquisition of the

The block sample is positioned under the SEM column.

whole 3D data stack, up to 32 k × 24 k image size, Gatan detector

After imaging the block face, move the sample up a small step,for high BSE signal, high vacuum compatible, motorized xy-move-

down to 15 nm. The ultramicrotome knife cuts the top of thement of the 3View® stage, allows two additional imaging modes:­sample and retracts, exposing a new block face. You can produce

Montage: automated volume acquisition of adjacent areas, Multi

thousands of serial images in a single day – each perfectly aligned

ROI: imaging of several user defined regions of interest.

because they are all generated from one fixed block.

Ultramicrotome 3View® (only Sigma VP):
Cut thickness down to 30 nm, automated image acquisition of thewhole 3D data stack, up to 32 k × 24 k image size, Gatan detector
for high BSE signal.

(* further electron microscopes available on request)

Software
SmartSEM, Gatan Microscopy Suite®

50

Mouse extraocular muscle with reconstructed peripheral nerves, 100 × 100 × 100

Mouse brain imaged with Sigma 3View, stack of 75 images with 7 nm pixels,

micrometer 3D dataset with 1,000 slices. Courtesy of P. Munro, University College

microtome set to remove 15 nm / slice. Courtesy of N. Kamasawa, Max Planck

London, UK

Florida Institute, USA and R. Shigemoto, National Institute for Physiological Sciences,
Okazaki, Japan

Simpler. More Intelligent. More Integrated.

Created for Your Applications• Enjoy the advantages of unmatched low voltage performance.

• Get high resolution 3D data of whole cells overnight.

• Operate in high vacuum mode without charging or use• Investigate the neuronal network and synapses ofthe variable pressure (VP) mode for charge neutralization.
• Eliminate unwanted signals from the depth of the sample.
• Avoid stage biasing.
• The large fields of view without distortions (32 k × 24 k)
reduce time-consuming stitching of many small images.

neurobiological samples.
• Enter the field of brain mapping by imaging huge sample
volumes in the shortest possible time.
• Acquire 3D images of your model organisms at different stagesof development.

• You will never need to compromise in resolution when using
high current modes.
• Get your 3D data up to 10 times faster – overnight insteadof over the week.

51

Electron Microscopy

ZEISS Atlas 5 Array Tomography:
The Fast and Easy Way to Image Your Serial Sections
Your Technology: Correlative Microscopy

Configured to Your Requirements
Image large areas and large amounts of serial sections inElectron Microscopes

the shortest possible time – it’s fully automated withAtlas 5 Array Tomography is available for all ZEISS SEMs.

Atlas 5 Array Tomography.

Recommended systems:
Sigma 300 / 500, GeminiSEM 300 / 500, Merlin,

Use its workflow-oriented graphical user interface to determine

Crossbeam 340 / 540 / 550

which areas of the sample you want to image automatically.
Define unlimited regions of interest with an arbitrary shape andHardware­assign different acquisition protocols. Pre-defined protocols help

Stand alone scan generator and image acquisiton module,

you acquire images easily at optimum conditions – even for ­d ifferent

PC, Monitor

resolutions and sample types. Use Atlas 5 Array T­ omography’sviewer to zoom seamlessly through your image data – from

Software­nanometers to centimeters – always at the most ­appropriate reso-

Atlas 5 Array Tomographylution. And it’s just as easy to import and align ­images from other

SmartSEM

sources, such as light optical images.

52

Large scale mosaic of a thick section of a rat brain, prepared with corrosion cast

Detail of large area image of a mosaic of ultrathin sectioned mouse brain on wafer,technique to reveal the blood vessels and their enveloping endothelium.

acquired with Atlas 5 Array Tomography.

Simpler. More Intelligent. More Integrated.

Created for Your Applications• Define regions of interest over hundreds of serial sections• Use standard sample preparation techniques to section yourwith different protocols – computer-assisted.
• Choose from the whole range of detectors including
STEM and BSE detectors.
• Acquire highly automated serial section images with automatedstage motion, focus, stigmation, brightness and contrast
adjustment.
• Image resolutions up to 32 k × 32 k pixels for the largest fieldsof view with high resolution – even at the edges.

sample onto grids, ITO-coated cover glasses or wafers.
• Histology: Investigate the 3D ultrastructure of tissue sample indifferent imaging modalities. You can preserve your sample andre-image selected regions at any time.
• Develop protocols to manage ideal imaging conditions efficiently
across resolutions and sample types. Ensure reproducibility andthe best possible images from your sample.
• Use light microscope images to guide navigation on your sample,• Use high imaging speed down to 25 ns dwell time per pixel.

then choose the most interesting regions for electron micro­­• The integrated Atlas 5 Array Tomography viewer lets you handle

scopy imaging. Overlay LM and EM data directly in Atlas 5 Arraygigapixel images and terapixel datasets efficiently with seamless

Tomography.

navigation and tools to align mosaics and correct image aber­rations.

53

X-ray Microscopy

Visualize Your Biological Specimens
in Their Native State in 3D

54

55

X-ray Microscopy

ZEISS Xradia Versa: Unparalleled Resolution and Contrast
Your Technology: X-ray Microscopy

Configured to Your Requirements
X-ray microscopy (XRM) lets you carry out vital analysis of hierar-

Microscopes

chical structures using non-destructive multi-length scale or multi-

Xradia 520 Versa, Xradia 510 Versa, Xradia 410 Versa

modal imaging of your sample. Examine internal structures at true
submicron-to-nanometer spatial resolution. You will achieve highTechniquecontrast in soft tissues and cells – often without requiring samples

X-ray microscopy

to be stained. Explore new applications using a technology that is
unique in the field of life sciences. 3D X-ray microscopes let you

Advanced Features

create a contextual 3D map to guide FIB-SEM and ultramicrotome-

Dual Scan Contrast Visualizer to image a sample at two different

based SEM techniques with great efficiency. Indeed, the emerging

X-ray spectra or in two different states, Automated Filter Changer

3D EM techniques will gain a significant boost in efficiency by(AFC), In situ Interface Kit to image materials under variable­imaging only the regions of interest.

environments with controlled conditions

56

Vasculature of intact mouse knee visible at high resolution at large working distance

Overall structure mapped at 50 µm, reduced to 0.5 µm to view surface of 20 µm
vessels

Simpler. More intelligent. More integrated.

Created for Your Applications• Profit from a spatial resolution of up to 700 nm.

• In osteoporosis research, see variations in bone structure at• With its powerful correlative capability, X-ray microscopy bridges
light and electron microscopy.
• Image stained and unstained tissue using both absorption
and phase contrast.
• Avoid tedious physical cross-sectioning and the risk of intro­
ducing artifacts or destroying information.
• Image samples under real world conditions, such as under
tensile loading or in hydrated environments.
• Maintain highest resolution 3D X-ray imaging at large working
distances for a wide range of sample sizes and shapes.

the same scale as individual cells. Understand how those cells
decide where to remove bone.
• Study structural changes in environmental models, including
fish, insects, and fossils, to understand the impact of toxins in
the environment and to help identify and confirm bioremediation
responses.
• Demonstrate the effectiveness of bio-scaffolding materials
and the ability for tissue to attach to implants.
• Investigate the impact of pharmaceutical solutions on cells
and even dentin.
• Correlate functional information to ultrastructure information
non-destructively.

57

Light Microscopy Combi Systems:
Individual Solutions for Challenging Research
Combining different optical sectioning and imaging
techniques offers you a unique route to gaining more
information from your sample. The modular concept
and the broad range of techniques available within
the portfolio make ZEISS a perfect choice for finding
the solution for your individual experimental design.
To safeguard your investment, many optical sectioning
technologies are also available as upgrades.
ZEISS Elyra PS.1
SR-SIM and PALM are complementary superresolution techniques with different pre­requirements for sample preparation. Combining them offers you the ability to overlay
the results of both imaging techniques to get a deeper understanding of your sample.
ZEISS LSM 8 Family with Airyscan and Elyra:
This combination offers maximum flexibility in terms of resolution and 3D acquisition.
Select the imaging technique required for your experiment without technical limitation.
This is the perfect instrument for a multi-user facility.
See page 36 for further information.
ZEISS Cell Observer SD and ZEISS DirectFRAP:
Full flexibility in live cell imaging with photomanipulation is available from the fast widefield laser sectioning systems on our powerful Axio Observer microscope.
Correlated Light and Electron Microscopy:
The optional Shuttle & Find module for correlative microscopy make it easy for you tomark an of interest in a light microscope and relocate it under a scanning electron microscope, unlocking their full analytical power and highest resolution for your samples.
See page 40 for further information.

59

Compare Light Microscopy Techniques
to Advance Your Research
Optical sectioning systems in light microscopy are flexible by definition, designed to handle
a wide range of sample types. Yet their capacity for a particular application does not lend
itself easily to direct comparison in tables. It’s impossible to say, for example, that the resolution of a multi­photon image will always be three times higher than that of an Apotome.2
image. You might be able to compare images of a clear sample, but not one from a dense,
highly scattering tissue: a multi­photon system will be capturing images at a depth that is
scarcely possible with Apotome.2. Thus tables can suggest how various microscopes per-form, but conditions differ from sample to sample and so will the relative performance.
The table on this page shows the relative performance of the light microscopy techniquefrom a technical perspective, highlighting the performance that the system is designed for.
The scale is not linear so two points will be better than one, but not necessarily twice as
good. Scores are comparable within the same row.

Relative Performances of the Techniques
Structured
DCV
ZEISS System

Illumination

Cell Observer Apotome.2

LSM
LSM 800

Light SheetSuperreso-

Superreso-

Airyscanning Illumination

lution PALM

lution SIM

Spinning Disk

Elyra S.1

Cell Ob­server

LSM 880

Lightsheet Z.1 Elyra P.1

with DCV

SD

Performance for
Out-of-focus











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

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



Depth penetration

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



Thin samples –



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



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



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























Acquisition speed

















Simple operation



















discrimination
Simultaneous multichannel
acquisition

lateral resolution
Thin samples –axial resolution
Thick samples –lateral resolution
Thick samples –axial resolution

  Suitable    

60

Particularly suitable

Expect This Level of Performance
for Typical Experiments
This table shows which light microscope systems are suitable for your experiments, but therelative scores can vary, depending on conditions. Think of them as guidelines. Your regional
ZEISS representative is ready to work with you to determine which systems will deliver thebest all-round performance for your specific samples, applications and area of research.

Experiments Compared
Structured
DCV
ZEISS system

Illumination

Cell Observer Apotome.2

LSM
LSM 800

Light SheetSuperreso-

Superreso-

Airyscanning Illumination

lution PALM

lution SIM

Spinning Disk

Elyra S.1

Cell Observer

LSM 880

Lightsheet Z.1 Elyra P.1

with DCV

SD

Performance forHigh-speed time-lapse













for vesicle tracking
Colocalization studies in





























































































30 µm tissue sections
4D imaging of mitotic
spindle division
Structural imaging of
Zebrafish or Drosophila
Simultaneous FRET
imaging
Very high-speed ion

imaging, e.g., calcium
imaging
Spectral flexibility











and removal of a­ utofluorescence
Neuronal imaging indeep live brain tissue
Photoactivation and / orbleaching, e.g., FRAP
Ultrastructural analysis
Cleared tissue imaging























  Suitable    

Particularly suitable

61

Technical Specifications
This table shows your numerous options for excitation, detection and photomanipulation ofyour fluorescent samples with the respective light microscope system for optical sectioning.

Structured
DCV

Illumination

CLSM

Airyscanning

Cell Observer

Apotome.2

LSM 800

LSM 880









Detector type
Camera, e.g.,
Axiocam MRm, HS,
EMCCD and sCMOS
Photomultiplier tubes



(PMT)
Non-descanneddetector (NDD)
Number of detection

1–2

1–2

2–3

3–36

1























channels
Excitation source
VIS laser
Widefield sources,

e.g., HBO, Colibri
Femtosecond pulsed
IR laser
Spectral detection
Sequential spectral imaging
Sequential spectraldetection and unmixing
Simultaneous spectraldetection and unmixing
Photomanipulation
Sequential arbitrary regionsof interest (ROI) with scanners
Optional simultaneous
photomanipulation ofwhole ROI with DirectFRAP(* LSM 800 only)

62







(*)

Light SheetSuperreso-

Superreso-

Illumination

lution PALM

lution SIM

Spinning Disk

Light­sheet Z.1

Elyra P.1

Elyra S.1

Cell Observer SD









1–2

1–2

1–2

1–2













Detector type
Camera, e.g.,
Axiocam MRm, HS,
EMCCD and sCMOS
Photomultiplier tubes(PMT)
Non-descanned
detector (NDD)
Number of detection
channels
Excitation source
VIS laser
Widefield sources,
e.g., HBO, Colibri
Femtosecond pulsed
IR laser
Spectral detection
Sequential spectral imaging

Sequential spectral
detection and unmixing
Simultaneous spectral
detection and unmixing
Photomanipulation
Sequential arbitrary regionsof interest (ROI) with scanners
Optional simultaneous

photomanipulation ofwhole ROI with DirectFRAP

63

Service and Support
for Your ZEISS Microscope System
ZEISS Moments are about passion. The same passionthat drives us to support and accompany you andyour ZEISS microscope over its life cycle makes surethat your work will lead systematically to success.

You Work Hard: We Make Sure Your Microscope Keeps Pace with You.
High imaging quality, reliable results and instrument availability are the parameters of yourday-to-day working life. Your ZEISS microscope integrates seamlessly into this demanding
workflow. It provides you with insights and results that you can trust: thorough, comprehensive and reproducible. With ZEISS Life Cycle Management we help you to keep yourmicroscope in optimum condition to get these optimum results.
Life Cycle Management Comes with Your MicroscopeLife Cycle Management from ZEISS backs up our solutions throughout the working life ofyour ZEISS microscope system. From the procurement phase onward, you can count on
our support, starting with site surveys to optimize the location for your microscope system. Throughout the operational phase we will complement our service with support forrelocations and upgrade opportunities that enhance or expand your possibilities. As soon
as you think about replacing your long-serving microscope with a new one, we will takecare of the disassembly and disposal of systems that are no longer needed. Rely on ourservice features: our employees analyse the status of your system and solve problems via
remote maintenance or directly at your location.
From Expert to Expert
Never hesitate to ask our application specialists to support your specific tasks. And be sure
to tap into our training sessions for any colleagues or employees who will be working withyour ZEISS microscope.
Peace of Mind and Availability with Regular MaintenanceYour service plan is tailor-made for you. Make sure you take advantage of all the oppor­
tunities your ZEISS microscope system offers. Get optimized performance, instrument­reliability and availability at predictable costs. Choose from different service levels of ourProtect Service Plans, ranging from Protect preventive, via Protect advanced, to Protect
premium. We look forward to discussing your ideal service plan personally.

65

// INSIGHT    MADE BY ZEISSThe moment you see something thathas been hidden from you until now.
This is the moment we work for.

How will doctors treat their patients in the future? How far can we go with the miniaturization of semiconductor structures? What role will photographs and videos play in theway we communicate in years to come? These and many other questions are what drive
us every day at ZEISS. Only those who ask will find the answers.
As pioneers in the industry and one of today’s worldwide leaders in the field of optics
and optoelectronics, we have always pushed the limits of the imagination at ZEISS.
The questions for medicine in the future are already being worked on by our people –with boldness, passion, and innovation. From this impetus will come medical instrumentsthat optimize the success of treatments and laboratory devices that will underpin medical
advances.
The many challenges that industry faces also motivate us to continue setting new standards
in technology. As we do, quality in all components is being safeguarded by ZEISS. Just as it
will be in the smaller, higher-performance and low-priced microchip of the future.
ZEISS researchers and developers are working with equal determination to realize their
quality standards for moving and fixed images. Whether in the largest planetarium in theworld or in the smallest smartphone that has ever been built, it’s going to happen and you
will see it. This passion for topmost performance links all business areas at ZEISS. That’s
how we create advantages for our customers and inspire the world to look for things thathave been hidden until now.

67

Carl Zeiss Microscopy GmbH07745 Jena, Germany
microscopy@zeiss.com
www.zeiss.com/3d-imaging
EN_41_010_020 | CZ 11-2017 | Subject to design changes and changes to contents included in delivery, as well as technological advancements. | © Carl Zeiss Microscopy GmbHNot for therapeutic, treatment or medical diagnostic evidence. Not all products are available in every country. Contact your local ZEISS representative for more information.